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To study the relation between the human Na(+)-H+ exchanger (NHE-1) and the renal brush border membrane (BBM) Na(+)-H+ exchanger, polyclonal antibodies to synthetic peptides representing a putative external (Ab-E) and an internal cytosolic domain (Ab-I) of human NHE-1 were generated in rabbits. Western immunoblot analyses indicated that both antibodies recognized a 97-kD protein in rabbit renal BBM but not basolateral membranes (BLM). Octyl glucoside-extracted rabbit renal BBM proteins also contained the 97-kD polypeptide as did a fraction eluted from an anion-exchange column with 0.2 M NaCl (fraction A). A fraction eluting between 0.2 and 0.4 M NaCl (fraction B) did not contain this protein. Prior reconstitution studies have indicated that Na(+)-H+ exchange activity is higher significantly in fraction B than fraction A. Administration of NH4Cl for 3-7 d to rabbits, a stimulus known to increase renal BBM Na(+)-H+ exchange activity, did not result in a change in expression of the 97-kD protein in either renal BBM or BLM. The results indicate that affinity-purified polyclonal antibodies to two separate domains of the human Na(+)-H+ exchanger recognize a 97-kD protein in rabbit renal BBM but not BLM. The dissociation between recognition of the 97-kD protein using antibodies and the majority of functional Na(+)-H+ exchange activity after chromatographic fractionation of solubilized BBM proteins and in native BBM after administration of NH4Cl suggest that rabbit renal BBM contains more than one form of Na(+)-H+ exchanger.